Human evolution tied to a small fraction of the genome – “Only about 7.5 percent of the human genetic instruction book shaped the evolution of human traits, a new study suggests. And it’s often not genes, but the how-to instructions for using those genes that are most important, researchers report January 19 in Nature Genetics…. Previously, researchers have mostly looked for evolutionary clues in protein-producing genes because proteins do much of the important work in cells and organisms. Altering a protein may change the way an organism looks or acts. But mutations that alter proteins often are devastating to an organism and therefore aren’t passed on to offspring. Gulko and colleagues found that only 9 percent of the DNA that got evolution’s attention resides in protein-coding parts of the genome that are shared with other species. About 52 percent of the places showing signs of natural selection were in intergenic regions, the stretches of DNA between genes. Another 35 percent were in introns — spacer DNA found within genes but not involved in encoding proteins. Both intergenic regions and introns often contain DNA responsible for controlling gene activity. These findings suggest that human evolution works mostly through changes in how genes are used, rather than by altering genes and the proteins they encode.”

Kennewick Man was Native American – “‘Genetic analysis is still under way in Denmark, but documents obtained through the federal Freedom of Information Act say preliminary results point to a Native-American heritage.'” – from dienekes. see also from razib: Native Americans Are Evolutionarily Elegant – “One insight of modern ancient DNA is that there has been a great deal of population turnover over the past ~10,000 years, as well as admixture between disparate lineages. When Kennewick Man died ~9,000 years ago Europeans as we understand them did not exist genetically.”

The Genetic Ancestry of African Americans, Latinos, and European Americans across the United States – “Over the past 500 years, North America has been the site of ongoing mixing of Native Americans, European settlers, and Africans (brought largely by the trans-Atlantic slave trade), shaping the early history of what became the United States. We studied the genetic ancestry of 5,269 self-described African Americans, 8,663 Latinos, and 148,789 European Americans who are 23andMe customers and show that the legacy of these historical interactions is visible in the genetic ancestry of present-day Americans. We document pervasive mixed ancestry and asymmetrical male and female ancestry contributions in all groups studied. We show that regional ancestry differences reflect historical events, such as early Spanish colonization, waves of immigration from many regions of Europe, and forced relocation of Native Americans within the US. This study sheds light on the fine-scale differences in ancestry within and across the United States and informs our understanding of the relationship between racial and ethnic identities and genetic ancestry.” – see also: The Fluidity of Race from greg cochran.

Largest-ever autism genome study finds most siblings have different autism-risk genes – “In the new study, Dr. Scherer’s team sequenced 340 whole genomes from 85 families, each with two children affected by autism. The majority of siblings (69 percent) had little to no overlap in the gene variations known to contribute to autism. They found that the sibling pairs shared the same autism-associated gene changes less than one third of the time (31 percent). The findings challenge long-held presumptions. Because autism often runs in families, experts had assumed that siblings with the disorder were inheriting the same autism-predisposing genes from their parents. It now appears this may not be true.” – h/t shrikant mantri!

Genetic mutation for metabolic disease identified within an Inuit population – “The disease in question, glycogen storage disease type IIIa, is caused by mutations in the AGL gene, leading to less-active glycogen-debranching enzymes. The disorder disrupts the body’s capacity to release sugar from glycogen, resulting in the formation of damaging glycogen deposits…. Glycogen storage disease IIIa affects around one in 100,000 people in North America. However, the researchers estimate that the disorder may affect around 1 in 2,500 people in Nunavik – the homeland of the Inuit in Quebec.” – maybe they should stick to eating seal blubber. srsly!

Admixture in the Americas: Admixture among US Blacks and Hispanics and academic achievement – “[W]e see the expected directions and order, for Blacks (who are mostly African), American admixture is positive and European is more positive…. We do not see the expected results per genetic model. Among Hispanics who are 73% European, African admixture has a positive relationship to academic achievement. American admixture is negatively correlated and European positively, but weaker than African. The only thing that’s in line with the genetic model is that European is positive. On the other hand, results are not in line with a null model either….” – from emil kirkegaard.

School – “In summary, it very much looks like more years of education are associated with an increase in intelligence test scores, but not anything like as strongly to underlying general intelligence or to underlying basic processing speeds.” – from dr. james thompson.

Genetic Pleiotropy Explains Associations between Musical Auditory Discrimination and Intelligence – “[A] large sample of Swedish twins (N = 10,500) was used to investigate the genetic architecture of the associations between intelligence and performance on three musical auditory discrimination tasks (rhythm, melody and pitch). Phenotypic correlations between the tasks ranged between 0.23 and 0.42 (Pearson r values). Genetic modelling showed that the covariation between the variables could be explained by shared genetic influences. Neither shared, nor non-shared environment had a significant effect on the associations. Good fit was obtained with a two-factor model where one underlying shared genetic factor explained all the covariation between the musical discrimination tasks and IQ, and a second genetic factor explained variance exclusively shared among the discrimination tasks. The results suggest that positive correlations among musical aptitudes result from both genes with broad effects on cognition, and genes with potentially more specific influences on auditory functions.” – h/t rosalind arden!

The Role of Parenting in the Prediction of Criminal Involvement: Findings From a Nationally Representative Sample of Youth and a Sample of Adopted Youth [pdf] – “The role of parenting in the development of criminal behavior has been the source of a vast amount of research, with the majority of studies detecting statistically significant associations between dimensions of parenting and measures of criminal involvement. An emerging group of scholars, however, has drawn attention to the methodological limitations — mainly genetic confounding — of the parental socialization literature. The current study addressed this limitation by analyzing a sample of adoptees to assess the association between 8 parenting measures and 4 criminal justice outcome measures. The results revealed very little evidence of parental socialization effects on criminal behavior before controlling for genetic confounding and no evidence of parental socialization effects on criminal involvement after controlling for genetic confounding.” – h/t jayman!

Hospitals Aim to Better Match Blood Donors and Recipients – “People fall into one of four main blood groups — A, B, AB and O — and they have a so-called Rh factor that is either positive or negative. But scientists over the last few decades have discovered around 33 blood groups and continue to identify more. Each group also contains multiple variations that go to make up a patient’s exact blood type.”

Ageing research: Blood to blood – “By splicing animals together, scientists have shown that young blood rejuvenates old tissues. Now, they are testing whether it works for humans.” – parabiosis. it’s baaaack!

Comparative analysis of the human saliva microbiome from different climate zones: Alaska, Germany, and Africa [pdf] – “Here we analyze the saliva microbiome from native Alaskans (76 individuals from 4 populations), Germans (10 individuals from 1 population), and Africans (66 individuals from 3 populations) based on next-generation sequencing of partial 16S rRNA gene sequences. After quality filtering, a total of 67,916 analyzed sequences resulted in 5,592 OTUs (defined at ≥97% identity) and 123 genera. The three human groups differed significantly by the degree of diversity between and within individuals (e.g. beta diversity: Africans > Alaskans > Germans; alpha diversity: Germans > Alaskans > Africans). UniFrac, network, ANOSIM, and correlation analyses all indicated more similarities in the saliva microbiome of native Alaskans and Germans than between either group and Africans. The native Alaskans and Germans also had the highest number of shared bacterial interactions.”

Tuberculosis genomes track human history – “A study of nearly 5,000 samples of Mycobacterium tuberculosis from around the world shows how a lineage of the bacterium that emerged thousands of years ago in Asia has since become a global killer that is widely resistant to antibiotic drugs. Although M. tuberculosis probably first emerged some 40,000 years ago in Africa, the disease did not take hold until humans took to farming…. [T]he common ancestor of all the M. bacterium strains circulating today began spreading around 10,000 years ago in the ancient Fertile Crescent, a region stretching from Mesopotamia to the Nile Delta that was a cradle of agriculture…. But of all the M. bacterium strains circulating today, few strike more fear in public-health officials than the ‘Beijing lineage’. First identified in greater Beijing in the mid-1990s, this lineage now circulates throughout the world and many strains are resistant to drugs that vanquish other types of TB…. Consistent with its name, the Beijing lineage did indeed emerge near north-eastern China…. And it did so around 6,600 years ago, the researchers found, which coincides with archaeological evidence for the beginnings of rice farming in China’s upper Yangtze River valley.” – h/t billare!

Your Friends Know How Long You Will Live: A 75-Year Study of Peer-Rated Personality Traits – “To test whether friends’ reports of personality predict mortality risk, we used data from a 75-year longitudinal study (the Kelly/Connolly Longitudinal Study on Personality and Aging). In that study, 600 participants were observed beginning in 1935 through 1938, when they were in their mid-20s, and continuing through 2013. Male participants seen by their friends as more conscientious and open lived longer, whereas friend-rated emotional stability and agreeableness were protective for women. Friends’ ratings were better predictors of longevity than were self-reports of personality, in part because friends’ ratings could be aggregated to provide a more reliable assessment.”

Voluntary Activities and Daily Happiness in the US [pdf] – “This paper analyzes differences in daily happiness between those individuals in the United States who perform voluntary activities during the day, and those who do not…. [T]hose who devote any time to voluntary activities during the day report higher levels of daily happiness than those who do not…. [W]hen the issue of reverse causality is taken into account, we find no differences in daily happiness between volunteers and non-volunteers, which indicates that happier individuals are also more likely to volunteer.” – h/t ben southwood!

Aberrant Gene Expression in Humans – “The uniqueness of individuals is due to differences in the combination of genetic, epigenetic and environmental determinants. Understanding the genetic basis of phenotypic variation is a key objective in genetics…. One of our major findings is that private SNPs may contribute to aberrant expression in outlier individuals. These private SNPs are more frequently located in the enhancer and promoter regions of genes that are aberrantly expressed, suggesting a possible regulatory function of these SNPs.”

Recurrent loss of sex is associated with accumulation of deleterious mutations in Oenothera – “Sexual reproduction is nearly universal among eukaryotes. Theory predicts that the rarity of asexual eukaryotic species is in part caused by accumulation of deleterious mutations and heightened extinction risk associated with suppressed recombination and segregation in asexual species. We tested this prediction with a large dataset of 62 transcriptomes from 29 species in the plant genus Oenothera, spanning 10 independent transitions between sexual and a functionally asexual genetic system called permanent translocation heterozygosity…. These results confirm that an important advantage of sex is that it facilitates selection against deleterious alleles, which might help to explain the dearth of extant asexual species.” – h/t melissa wilson sayres!

Lewontin wins the Crafoord Prize – “The Crafoord Prize for 2015 was awarded to Richard Lewontin and Tomoko Ohta, for their discovery that there was very much more genetic variation that had been expected. Lewontin discovered this using protein gel electrophoresis to study a number of loci in Drosophila. It’s an important result. The problem is, virtually everything he’s said and done since that time has been a pile of steaming ideological crap.” – from greg cochran.

Single Markers Tell You Only a Bit About Individual Ancestry – “A new paper in The American Journal of Human Genetics, Estimates of Continental Ancestry Vary Widely among Individuals with the Same mtDNA Haplogroup, tells you something which should be obvious: one marker tells you only so much about individual ancestry. In other words, the history of one gene can only tell you so much about the whole genome. Because mtDNA and Y chromosome* does not recombine you can treat it as one long genetic marker…. But Richard Lewontin’s insight that a great deal of human genetic variation is not partitioned across populations, but within them, applies to mtDNA and the Y chromosomes as well. Where Lewontin’s insight misleads is that using just a few more markers one can obtain relatively robust phylogenetic trees which reflect well the population structure and history of a given species.” – also from razib.

The Economist takes a half step forwards – “They do not examine the usual finding that educated parents are more influential than rich parents in supposedly ‘boosting’ intelligence. They leave out the genetic element entirely, and say it is ‘incomes’ which are inherited. If so adoption into a rich household should have massive effects on intellect, but that is not found. If adoption cannot wipe the slate clean, what chance a kindergarten?” – from dr. james thompson.

Gender divide in religious belief, survey suggests – “A big gender divide exists between men and women in their 40s in belief in God and life after death, a poll suggests. Of the British men surveyed, 54% said they were atheists or agnostics compared with only 34% of women. The study also showed that Muslims in the survey had the fewest doubts about the existence of God and the afterlife. The research involving more than 9,000 British people born in 1970 was analysed at the University of Essex.” – h/t ed west! who tweeted: “71% of evangelical Christians have no doubts about God’s existence. 33% of Catholics, 16% of Anglicans & Methodists.”

Thumb bones in pre-humans make them more like us, study says – “Some of our tree-swinging pre-human ancestors may have been a bit more like us than previously thought, thanks to a tiny section of their thumbs. One key attribute that separates humans from other animals is our opposable thumb, and the way parts of the thumb are structured to allow for a strong yet precise grip that fostered advanced use of tools. It’s what allows us to throw items more precisely, pick guitars and turn a key. And now, thanks to high-tech tools of our own, scientists have determined that a couple million years ago one of our pre-human ancestors had the same human-defining precision grip, even though researchers think of them as little more than upright walking apes, according to a study published Thursday in the journal Science. That supports earlier but controversial evidence that the small-brained Australopithecus africanus fashioned early tools.” – h/t regular ron!

Thomas Cromwell was the Islamic State of his day – “No one can be sure of the exact figure, but it is estimated that the destruction started and legalised by Cromwell amounted to 97% of the English art then in existence. Statues were hacked down. Frescoes were smashed to bits. Mosaics were pulverized. Illuminated manuscripts were shredded. Wooden carvings were burned. Precious metalwork was melted down. Shrines were reduced to rubble.”

bonus bonus bonus bonus bonus: All in the (bigger) family – “A decade of genetic data and other evidence has persuaded most researchers that insects and crustaceans, long considered widely separated branches of the arthropod family, actually belong together. The new arthropod tree puts hexapods — six-limbed creatures that include insects, springtails, and silverfish — as closer kin to crabs, lobster, shrimp, and crayfish than those ‘standard’ crustaceans are to others such as seed shrimp.”

and, incidently, sex. from The Ancestor’s Tale — h/t to the person who linked to this on twitter the other evening. i forgot who it was! (*^_^*) (sorry!) [pgs. 406-408 — links added by me]:

“It is genuinely true that, if you measure the total variation in the human species and then partition it into a between-race component and a within-race component, the between-race component is a very small fraction of the total. Most of the variation among humans can be found within races as well as between them. Only a small admixture of extra variation distinguishes races from each other. That is all correct. What is not correct is the inference that race is therefore a meaningless concept. This point has been clearly made by the distinguished Cambridge geneticist A. W. F. Edwards in a recent paper called ‘Human genetic diversity: Lewontin’s fallacy’. R. C. Lewontin is an equally distinguished Cambridge (Mass.) geneticist, known for the strength of his political convictions and his weakness for dragging them into science at every possible opportunity. Lewontin’s view of race has become near-universal orthodoxy in scientific circles. He wrote, in a famous paper of 1972:

“‘It is clear that our perception of relatively large differences between human races and subgroups, as compared to the variation within these groups, is indeed a biased perception and that, based on randomly chosen genetic differences, human races and populations are remarkably similar to each other, with the largest part by far of human variation being accounted for by the differences between individuals.’

“This is, of course, exactly the point I accepted above, not surprisingly since what I wrote was largely based on Lewontin. But see how Lewontin goes on:

“‘Human racial classification is of no social value and is positively destructive of social and human relations. Since such racial classification is now seen to be of virtually no genetic or taxonomic significance either, no justification can be offered for its continuance.’

“We can all happily aggree that human racial classification is of no social value and is positively destructive of social and human relations. That is one reason why I object to ticking boxes in forms and why I object to positive discrimination in job selection. But that doesn’t mean that race is of ‘virutally no genetic or taxonomic significance’. This is Edwards’s point, and he reasons as follows. However small the racial partition of the total variation may be, if such racial characteristics as there are are highly correlated with other racial characteristics, they are by definition informative, and therefore of taxonomic significance.

“Informative mean something quite precise. An informative statement is one that tells you something you didn’t know before. The information content of a statement is measured as reduction in prior uncertainly. Reduction in prior uncertainty, in turn, is measured as a change in probabilities…. If I tell you Evelyn is male, you immediately know a whole lot of things about him. Your prior uncertainty about the shape of his genitals is reduced (though not obliterated). You now know facts you didn’t know before about his chromosomes, his hormones and other aspects of his biochemistry, and there is a quantitative reduction in your prior uncertainty about the depth of his voice, and the distribution of his facial hair and of his body fat and musculature….

“Now to the question of race. What if I tell you Suzy is Chinese, how much is your prior uncertainty reduced? You now are pretty certain that her hair is straight and black (or was black), that her eyes have an epicanthic fold, and one or two other things about her. If I tell you Colin is ‘black’ this does not, as we have seen, tell you he is black. [he might be mixed race.-h.chick] Nevertheless, it is clearly not uninformative. The high inter-observer correlation suggests that there is a constellation of characteristics that most people recognise, such that the statement ‘Colin is black’ really does reduce prior uncertaintly about Colin. It works the other way around to some extent. If I tell you Carl is an Olympic sprinting champion, your prior uncertainty about his ‘race’ is, as a matter of statistical fact, reduced. Indeed, you can have a fairly confident bet that he is ‘black’.”

of course, don’t forget: there’s more to human biodiversity than just racial differences! see: most of this blog.

Genomics England – “This project will sequence the personal DNA code – known as a genome – of up to 100,000 patients over the next five years.”

Your Genome Is a Post-Apocalyptic Wasteland – “Your 25,000 genes reside in a genetic landscape littered with the rubble of ancient and ongoing battles with hordes of viruses, clone armies of genetic parasites, and zombie genes that should be dead but aren’t. Our messy genomic landscape is a dynamic, miniature ecosystem, and scientists are learning how its inhabitants play a big role in human health and disease.”

Morality and the Perspicuity of the True Believers – “Consider, for example, a piece Dennis Prager just wrote for National Review Online, packaged as ‘A Response to Richard Dawkins.’ Prager cuts to the chase with the following: ‘If there is no God, the labels “good” and “evil” are merely opinions. They are substitutes for “I like it” and “I don’t like it.” They are not objective realities.’ Thank you, Mr. Prager. I couldn’t have said it better myself.” (^_^) – from helian.

Migration from Sweden to Poland during the Early Bronze Age – “‘”Over 3800 years ago, a young male, possibly born in Skåne, made a journey of over 900 kilometers south, to Wroclaw in Poland. He died violently in Wroclaw, killed by Úněticean farmers, possibly due to romance with two local females, who were murdered together with him.”‘” @dienekes’.

Please Pass the Microbes – “Once the animal had been processed more or less, I was amazed to see all three [hadza] men take a handful of the partially digested plant material from the recently removed stomach to scrub off the copious amounts of blood that now covered there hands and foreman’s. This was followed by a final ‘cleaning’ with dry grass for good measure. While I was fascinated by the microbe-laden stomach contents being used as hand scrubber – presumably transferring an extraordinary diversity of microbes from the Impala gut to the hands of the Hadza – I was not prepared for what they did next….” – you’ve GOT to read this! (^_^) – h/t john durant!

First physical evidence of why you’re an owl or a lark – “They found a reduction in the integrity of night owls’ white matter – brain tissue largely comprised of fatty insulating material that speeds up the transmission of nerve signals – in areas associated with depression. ‘We think this could be caused by the fact that late chronotypes suffer from this permanent jet lag,’ says Rosenberg, although she cautions that further studies are needed to confirm cause and effect.”

Human brain boiled in its skull lasted 4000 years – “Seyitömer Höyük – the Bronze Age settlement in western Turkey where this brain was found – is not in the mountains. So how did brain tissue survive in four skeletons dug up there between 2006 and 2011?”

Alien DNA could be ‘recreated’ on earth – “Humans will be able to recreate alien life forms and ‘print out’ organisms using the biological equivalent of a 3D printer in the future, a DNA pioneer has predicted.” – craig venter.

Loci number and group difference – “This paper shows that the debate about ‘variation within races is bigger than variation between races’ depends largely on the number of loci being analysed, and the assumptions being made about the significance of the revealed differences.” – from dr. james thompson.

Human Hair Confirmed in Prehistoric Hyena Feces – “The fossilized dung, part of a ‘hyena latrine,’ will be described in the upcoming October issue of the Journal of Archaeological Science…. Our ancestors there lived around a literally wild bunch about 257,000 years ago.” – #PaleoDiet! (O_O)

Academic fraud in China is getting out of hand – “In a few short years, China has metamorphosed from a middling contributor to scientific knowledge into one of the most prolific research entities on the planet. But the country’s meteoric ascent to scientific prominence – widely attributed to a flawed incentive system – has given unintentional rise to a lucrative industry of academic fakery.” – see also: Looks good on paper @the economist.

Poll Shows Major Shift in Identity of U.S. Jews – “The first major survey of American Jews in more than 10 years finds a significant rise in those who are not religious, marry outside the faith and are not raising their children Jewish — resulting in rapid assimilation that is sweeping through every branch of Judaism except the Orthodox.”

Electric Shock Therapy May Cut Crime By Stimulating Brain Region For Social Norm Compliance – “An original way to reduce crimes rates could lie in regulating neural activity in a person’s front of the brain — right lateral prefrontal cortex. Scientists from the University of Zurich have found a brain mechanism responsible for social norm compliance is separate from the processes that represents a person’s knowledge and beliefs about societal norms. The neurons in this specific brain region may be controlled by electric shock therapy which could potentially stop criminals from breaking the law….” – see also: Brain Stimulation Can Control Compliance with Social Norms – “Human beings are utterly dependent on a complex social structure for their survival. Since all behavior is controlled by the brain, human beings may have evolved specialized neural circuits that are responsible for compliance with society’s rules.” h/t михаи́л анисимов!

Latitude, elevation and the tempo of molecular evolution in mammals – “[B]ecause climatic variables change with latitude and elevation in a similar manner, our results suggest that climate has influenced the tempo of genetic change in mammals…. These findings provide new insights into microevolution that are likely to have important implications for understanding global patterns of biodiversity and diversification.”

An Asian perspective on early human dispersal from Africa – “Asia might not have been the passive recipient of whatever migrated out of Africa but might have been a major donor to speciation events, as well as dispersals back into Africa. Such two-way traffic is well documented for other mammals in the Pliocene and Early Pleistocene, such as Equus and bovids, with more taxa migrating into than out of Africa. There is no reason why hominin migrations were always from Africa into Asia, and movements in the opposite direction might also have occurred, as has been suggested for the Olduvai OH9 (refs 13, 58) and Daka specimens. We should even allow for the possibility that H. ergaster originated in Asia and perhaps explain its lack of an obvious east African ancestry as the result of immigration rather than a short (and undocumented) process of anagenetic (in situ) evolution (Dennell and Roebroeks 2005:1100-1101).” – see also: Did Early Humans First Arise in Asia, Not Africa?

Recent acceleration of human adaptive evolution – “It is sometimes claimed that the pace of human evolution should have slowed as cultural adaptation supplanted genetic adaptation…. Cultural changes have reduced mortality rates, but variance in reproduction has continued to fuel genetic change. In our view, the rapid cultural evolution during the Late Pleistocene created vastly more opportunities for further genetic change, not fewer, as new avenues emerged for communication, social interactions, and creativity.” – hawks, wang, cochran, harpending & moyzis.

Human genetic diversity: Lewontin’s fallacy [opens pdf] – “In popular articles that play down the genetical differences among human populations, it is often stated that about 85% of the total genetical variation is due to individual differences within populations and only 15% to differences between populations or ethnic groups. … This conclusion, due to R.C. Lewontin in 1972, is unwarranted because the argument ignores the fact that most of the information that distinguishes populations is hidden in the correlation structure of the data and not simply in the variation of the individual factors.”

The Misguided Advocates of Open Borders – “Rising diversity within human societies tends to drive people apart, causing them to take sanctuary in individual pursuits and ethnic communities. The practical consequences are reduced public altruism or social capital, evident in falling volunteerism, government welfare for the aged and sick, public health care and a general loss of trust. Ethnic diversity is second only to lack of democracy in predicting civil war. Globally it correlates negatively with governmental efficiency and prosperity.” – frank salter.

“It is not unusual for people to sort one another into group categories by external characteristics including ethnicity, language, skin color, and morphological features. These people sorting mechanisms neglect genetic similarities as well as many nonobservable genetic differences. In the early 1970s scientists began studying how different population groups varied genetically. It became evident in the early 1970s, through a path-breaking study by Richard Lewontin, that there was more genetic diversity within a population group (e.g., West Africans) than between two groups (West Africans and Europeans).“